--- a +++ b/docs/installation.md @@ -0,0 +1,62 @@ +```{highlight} shell + +``` + +# Installation + +## Stable release + +To install ehrapy, run this command in your terminal: + +```console +pip install ehrapy +``` + +This is the preferred method to install ehrapy, as it will always install the most recent stable release. + +If you don't have [pip] installed, this [Python installation guide] can guide you through the process. + +If you run into "RuntimeError: CMake must be installed to build qdldl" ensure that you have CMake installed to build lightgbm. +Run `conda install -c anaconda cmake` and `conda install -c conda-forge lightgbm` to do so. + +If you intend to run MedCAT you have to install a language model like: + +```console +python -m spacy download en_core_web_sm +``` + +## From sources + +The sources for ehrapy can be downloaded from the [Github repo]. + +You can either clone the public repository: + +```console +git clone git://github.com/theislab/ehrapy +``` + +Or download the [tarball]: + +```console +curl -OJL https://github.com/theislab/ehrapy/tarball/master +``` + +## MedCAT/Spacy language models + +If you want to run and use medcat with ehrapy, you first have to install the medcat extra: + +```console +pip install ehrapy[medcat] +``` + +Available language models are + +- en_core_web_md (python -m spacy download en_core_web_md) +- en-core-sci-sm (pip install <https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.4.0/en_core_sci_sm-0.4.0.tar.gz>) +- en-core-sci-md (pip install <https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.4.0/en_core_sci_md-0.4.0.tar.gz>) +- en-core-sci-lg (pip install <https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.4.0/en_core_sci_lg-0.4.0.tar.gz>) + +[github repo]: https://github.com/theislab/ehrapy +[pip]: https://pip.pypa.io +[python installation guide]: http://docs.python-guide.org/en/latest/starting/installation/ +[tarball]: https://github.com/theislab/ehrapy/tarball/master